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- PDB-2jqn: Solution NMR structure of CC0527 from Caulobacter crescentus. Nor... -

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Basic information

Entry
Database: PDB / ID: 2jqn
TitleSolution NMR structure of CC0527 from Caulobacter crescentus. Northeast Structural Genomics Target CCR55
ComponentsHypothetical protein
KeywordsSTRUCTURAL GENOMICS / solution NMR structure / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyProtein of unknown function DUF952 / Protein of unknown function DUF952 / Protein of unknown function (DUF952) / ADP-ribosylation fold / Alpha-Beta Barrel / Alpha Beta / DUF952 domain-containing protein
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsAramini, J.M. / Rossi, P. / Moseley, H.N.B. / Wang, D. / Nwosu, C. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. ...Aramini, J.M. / Rossi, P. / Moseley, H.N.B. / Wang, D. / Nwosu, C. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of CC0527 from Caulobacter crescentus
Authors: Aramini, J.M. / Rossi, P. / Moseley, H.N.B. / Wang, D. / Nwosu, C. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T.
History
DepositionJun 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.6May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)13,5291
Polymers13,5291
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Hypothetical protein /


Mass: 13529.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: CC0527 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: UniProt: Q9AAR9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-13C NOESY
1513D 1H-13C NOESY aromatic
1623D 1H-13C NOESY
1713D HNCO
1813D HN(CA)CO
1913D HN(CO)CA
11013D HNCA
11113D GFT HNNCACBCA
11213D GFT CACB(CO)NHN
11313D GFT HAHBCACB(CO)NHN
11413D (H)CCH-TOCSY
11513D (H)CCH-COSY
11613D CCH-TOCSY
11713D HNHA
11832D 1H-13C HSQC high res.
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE AND GFT NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE AND GFT NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE, DIHEDRAL ANGLE (HYPER) AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 97.6%, SIDE CHAIN, 96.5%, AROMATICS, 89.1%, STEREOSPECIFIC METHYL, 91.3%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 116, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 3-22,26-31,34-35,40-49,56-62,69-73,80-96,109-112: (A) RMSD (ORDERED RESIDUES): BB, 0.9, HEAVY ATOM, 1.3. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 91.3%, ADDITIONALLY ALLOWED, 8.7%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.25/-0.67, ALL, -0.15/-0.89. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 19.99/-1.90. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-116): RECALL, 0.985, PRECISION, 0.900, F-MEASURE, 0.941, DP-SCORE, 0.755. THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED (S(PHI) + S(PSI) < 1.8): 1-2,23-25,32-33,36-39,50-55,63-68,74-79,97-108,113-116.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3, 95% H2O/5% D2O95% H2O/5% D2O
20.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3, 100% D2O100% D2O
30.58 mM [U-5% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.98 mMCcR55[U-100% 13C; U-100% 15N]1
20 mMMES1
100 mMNaCl1
5 mMCaCl21
10 mMDTT1
0.02 %NaN31
0.98 mMCcR55[U-100% 13C; U-100% 15N]2
20 mMMES2
100 mMNaCl2
5 mMCaCl22
10 mMDTT2
0.02 %NaN32
0.58 mMCcR55[U-5% 13C; U-100% 15N]3
20 mMMES3
100 mMNaCl3
5 mMCaCl23
10 mMDTT3
0.02 %NaN33
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
AutoAssign2.2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
Sparky3.11Goddardpeak picking
Sparky3.11Goddarddata analysis
AutoStructure2.1.1Huang, Tejero, Powers and Montelionestructure solution
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIH2.11.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.11.2Schwieters, Kuszewski, Tjandra and Clorerefinement
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.3Bhattacharya and Montelionedata analysis
PdbStat5Tejero and Montelionepdb analysis
VNMR6.1CVariancollection
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1164 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 108 DIHEDRAL ANGLE CONSTRAINTS, AND 66 HYDROGEN BOND CONSTRAINTS (11.7 CONSTRAINTS ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1164 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 108 DIHEDRAL ANGLE CONSTRAINTS, AND 66 HYDROGEN BOND CONSTRAINTS (11.7 CONSTRAINTS PER RESIDUE, 3.6 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 116 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR-NIH). AFTER A FINAL XPLOR CALCULATION USING THE CONSTRAINTS DERIVED FROM AUTOSTRUCTURE, THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYANMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS).
NMR constraintsNOE constraints total: 1164 / NOE intraresidue total count: 221 / NOE long range total count: 375 / NOE medium range total count: 244 / NOE sequential total count: 324
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 2.1 ° / Maximum upper distance constraint violation: 0.17 Å
NMR ensemble rmsDistance rms dev: 0.01 Å

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